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Yorodumi- PDB-6k1g: Crystal structure of the L-fucose isomerase soaked with Mn2+ from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k1g | ||||||
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Title | Crystal structure of the L-fucose isomerase soaked with Mn2+ from Raoultella sp. | ||||||
Components | L-fucose isomerase | ||||||
Keywords | ISOMERASE / fucose | ||||||
Function / homology | Function and homology information L-fucose isomerase / L-fucose isomerase activity / L-fucose catabolic process / manganese ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Raoultella planticola (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å | ||||||
Authors | Kim, I.J. / Kim, D.H. / Nam, K.H. / Kim, K.H. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Biotechnol Biofuels / Year: 2019 Title: Enzymatic synthesis of l-fucose from l-fuculose using a fucose isomerase fromRaoultellasp. and the biochemical and structural analyses of the enzyme. Authors: Kim, I.J. / Kim, D.H. / Nam, K.H. / Kim, K.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k1g.cif.gz | 661.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k1g.ent.gz | 547.3 KB | Display | PDB format |
PDBx/mmJSON format | 6k1g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6k1g_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 6k1g_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 6k1g_validation.xml.gz | 117.8 KB | Display | |
Data in CIF | 6k1g_validation.cif.gz | 161.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k1/6k1g ftp://data.pdbj.org/pub/pdb/validation_reports/k1/6k1g | HTTPS FTP |
-Related structure data
Related structure data | 6k1fC 1fuiS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 67347.219 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: GB MK893986 / Source: (gene. exp.) Raoultella planticola (bacteria) / Gene: fucI, NCTC13095_01108 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A377T0E7, UniProt: A0A443VNT1*PLUS, L-fucose isomerase #2: Chemical | ChemComp-MN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.03 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES, PEG10000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9796 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 29, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→30 Å / Num. obs: 73180 / % possible obs: 93.8 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.058 / Rrim(I) all: 0.134 / Net I/σ(I): 17.343 |
Reflection shell | Resolution: 2.95→3 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 2.293 / Num. unique obs: 3296 / Rpim(I) all: 0.268 / Rrim(I) all: 0.539 / % possible all: 85.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FUI Resolution: 2.96→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.896 / SU B: 22.208 / SU ML: 0.392 / Cross valid method: THROUGHOUT / ESU R Free: 0.486 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.357 Å2
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Refinement step | Cycle: 1 / Resolution: 2.96→30 Å
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Refine LS restraints |
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